Home

Workshop Outline

In this workshop, we will be working through the following sections, which can also be accessed via the sidebar.

• Getting Started

  • Download materials and get working space ready

• Introduction to RNA-Seq

• Quality Control of RNA-Seq Reads

  • Procedures for diagnosing and fixing problems in the raw sequence data
  • Tools: FastQC, Trimmomatic

• Alignment of RNA-Seq Reads to Reference Genome

  • Map the cleaned-up sequencing reads to appropriate regions on the reference genome
  • Tools: Bowtie/Tophat, Samtools

• Expression Quantification

  • Count the number of reads that are mapped to annotated genomic features
  • Tools: summarizeOverlaps() R function

• Differential Expression Analysis

  • Given two groups of interest, perform statistical tests of differential expression for each genomic feature
  • Tools: edgeR